Novel Genomic Tools to Assess Fish Diet and Prey Quality and in the Choptank River

Principal Investigator:

Louis Plough

Start/End Year:

2018 - 2020


Horn Point Laboratory, University of Maryland Center for Environmental Science

Co-Principal Investigator:

Jamie Pierson, Horn Point Laboratory, University of Maryland Center for Environmental Science


Strategic focus area:

Sustainable fisheries and aquaculture


Zooplankton are critical food sources for marine fish, and climate-driven changes in their abundance, diversity, and quality can have profound effects on larval recruitment and fisheries productivity in coastal oceans and estuaries. Despite the importance of prey for understanding variation in fisheries recruitment, accurate identification of zooplankton species remains challenging and a lack of information on prey quality and prey selectivity by fish may hinder the discovery of relationships between zooplankton and fish productivity. In Chesapeake Bay, two copepods, Acartia tonsa and Eurytemora carolleeae, are critical components of bay anchovy (Anchoa mitchili), larval striped bass (Morone saxatilis), and other fish diets. However, the relative prey quality of these and other zooplankton species in Chesapeake Bay is poorly characterized, and current approaches to quantify zooplankton lack sufficient taxonomic resolution to distinguish known cryptic lineages in A. tonsa, which may differ substantially in prey quality. Novel approaches are needed to resolve taxonomy among zooplankton, to determine diet selectivity, and to measure prey quality, information which will advance our understanding of how the prey field affects recruitment variation in these commercially and ecologically significant species.

In this proposal, we seek to characterize how changes in environmental variables influence fish diets and zooplankton abundance, distribution, and quality (lipids) in the Choptank River, using cutting-edge genomic barcoding and lipid analysis approaches. We will quantify the diversity of zooplankton in the field and in fish gut contents, placing particular focus on the two dominant prey items, E. carolleeae and A. tonsa. For those target prey species, we will track variation in prey quality based on individual size and lipid content. By synthesizing gut contents, zooplankton composition and diversity, prey quality, and environmental data, we will produce novel zooplankton prey indices informed by the biology of the prey items and their importance in observed fish diets. These indices will be compared with fisheries productivity data from the MD DNR Juvenile Recruitment Indices, using data collected for this project and with historical zooplankton datasets (where possible) in step-wise regression models. Our goal is to determine which measurements of abundance and food quality are most important for developing useful indices for fisheries management, and to assess the efficacy of a genomic metabarcoding approach for characterizing zooplankton composition for monitoring efforts. To that end, we will specifically compare the cost and accuracy as well as the taxonomic resolution of the results of metabarcoding to more traditional microscopic identification and enumeration.

A major outcome of this project is hoped to be the implementation of these novel techniques for future monitoring efforts in the Chesapeake Bay region, which will be communicated to policymakers, managers, and stakeholders from MD DNR and NOAA through a workshop and best-practices document. Additionally, a new partnership with Chesapeake College will provide opportunities for undergraduates to engage in a comprehensive field/lab research experience, learning cutting-edge molecular techniques in zooplankton and fisheries ecology and providing college credit through an internship class.

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